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1 data prep spatial layers

read in some data A and data B. Modify some things, and save as layer 1.

2 data prep other layers

This sources a script that modifies another new layer (tableC) and saves it as table2 and table3, external to the direct Rmd path. It also sources a separate script that reads a previously-saved layer (table 1) and gapfills, saving as table1a.

3 model

sourced script reads in layers 1a, 2, and 3, and does some stuff, and saves the results as layers D and E.


5 Provenance

run_id run_tag run_date parent_fn file_loc filetype commit_url commit_author commit_date uncommitted_changes elapsed_time memory_use sys_info ses_info base_pkgs attached_pkgs rdf_subject rdf_object rdf_predicate run_hash
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/tableA.csv input https://github.com/OHI-Science/ohibc/commit/8b48c047ef11e01d13c8b61e83e8edc6cce99cf9 Casey O’Hara ohara@nceas.ucsb.edu Sat Apr 30 12:01:16 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/tableA.csv ~/github/ohibc/rmd_testing/./0_sample_script.Rmd prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/tableA2.csv input no version control info found NA NA TRUE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/tableA2.csv ~/github/ohibc/rmd_testing/./0_sample_script.Rmd prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/tableB.csv input https://github.com/OHI-Science/ohibc/commit/00b6e10615d39b60a92958f7d8887c9e1091af54 Casey O’Hara ohara@nceas.ucsb.edu Sat Apr 30 10:25:32 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/tableB.csv ~/github/ohibc/rmd_testing/./0_sample_script.Rmd prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/table1.csv output Previous commit: https://github.com/OHI-Science/ohibc/commit/893b6768bfa73aae999c60b5c61cdfd2e501944e Casey O’Hara ohara@nceas.ucsb.edu Fri Nov 13 11:03:56 2015 -0800 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/table1.csv prov:wasGeneratedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/1_data_prep_sample.R ~/github/ohibc/rmd_testing/tableC.csv input https://github.com/OHI-Science/ohibc/commit/00b6e10615d39b60a92958f7d8887c9e1091af54 Casey O’Hara ohara@nceas.ucsb.edu Sat Apr 30 10:25:32 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/tableC.csv ~/github/ohibc/rmd_testing/1_data_prep_sample.R prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/1_data_prep_sample.R ~/github/ohibc/rmd_testing/table3.csv output Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/1_data_prep_sample.R ~/github/ohibc/rmd_testing/table3.csv prov:wasGeneratedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/1_data_prep_sample.R ~/github/ohibc/rmd_testing/table2.csv output Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/1_data_prep_sample.R ~/github/ohibc/rmd_testing/table2.csv prov:wasGeneratedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/1a_gapfill.R ~/github/ohibc/rmd_testing/table1.csv input https://github.com/OHI-Science/ohibc/commit/893b6768bfa73aae999c60b5c61cdfd2e501944e Casey O’Hara ohara@nceas.ucsb.edu Fri Nov 13 11:03:56 2015 -0800 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/table1.csv ~/github/ohibc/rmd_testing/1a_gapfill.R prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/1a_gapfill.R ~/github/ohibc/rmd_testing/table1a.csv output Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/1a_gapfill.R ~/github/ohibc/rmd_testing/table1a.csv prov:wasGeneratedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/1_data_prep_sample.R ~/github/ohibc/rmd_testing/1a_gapfill.R sourced_script https://github.com/OHI-Science/ohibc/commit/725220e3bd1b4cc62bf54e26091504ca5aff6b0e Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 17:03:26 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/1_data_prep_sample.R ~/github/ohibc/rmd_testing/1a_gapfill.R prov:wasExecutedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/1_data_prep_sample.R sourced_script https://github.com/OHI-Science/ohibc/commit/c265b263de2b0d301dc5e251417e6447e2d42fde Casey O’Hara ohara@nceas.ucsb.edu Thu May 5 12:26:36 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/1_data_prep_sample.R prov:wasExecutedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/2_model_sample.R ~/github/ohibc/rmd_testing/table1a.csv input https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/table1a.csv ~/github/ohibc/rmd_testing/2_model_sample.R prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/2_model_sample.R ~/github/ohibc/rmd_testing/table2.csv input https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/table2.csv ~/github/ohibc/rmd_testing/2_model_sample.R prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/2_model_sample.R ~/github/ohibc/rmd_testing/table3.csv input https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/table3.csv ~/github/ohibc/rmd_testing/2_model_sample.R prov:used 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/2_model_sample.R ~/github/ohibc/rmd_testing/tableD.csv output Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/2_model_sample.R ~/github/ohibc/rmd_testing/tableD.csv prov:wasGeneratedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/2_model_sample.R ~/github/ohibc/rmd_testing/tableE.csv output Previous commit: https://github.com/OHI-Science/ohibc/commit/a7e123bbd5a648fafcb65ca901de0086c7e595eb Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 16:14:15 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/2_model_sample.R ~/github/ohibc/rmd_testing/tableE.csv prov:wasGeneratedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/2_model_sample.R sourced_script https://github.com/OHI-Science/ohibc/commit/725220e3bd1b4cc62bf54e26091504ca5aff6b0e Casey O’Hara ohara@nceas.ucsb.edu Tue May 3 17:03:26 2016 -0700 FALSE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/2_model_sample.R prov:wasExecutedBy 17f7dda5322432bc18624f3988f80d63290ec7d6
24 standard run Thu May 5 12:35:55 2016 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/./0_sample_script.Rmd parent_script https://github.com/OHI-Science/ohibc/commit/c265b263de2b0d301dc5e251417e6447e2d42fde Casey O’Hara ohara@nceas.ucsb.edu Thu May 5 12:26:36 2016 -0700 TRUE 4.558 NA System: Darwin, Release: 14.5.0. Machine: x86_64. User: caseyohara. R version: R version 3.2.4 (2016-03-10), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.10.5 (Yosemite). Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3 ~/github/ohibc/rmd_testing/./0_sample_script.Rmd ~/github/ohibc/rmd_testing/./0_sample_script.Rmd prov:wasDerivedFrom 17f7dda5322432bc18624f3988f80d63290ec7d6

Provenance summary for run 24 (17f7dda): standard run (Thu May 5 12:35:55 2016)
file_name file_dir filetype uncomm_chgs commit_hash
table1.csv /Users/caseyohara/github/ohibc/rmd_testing input FALSE 893b676
table1a.csv /Users/caseyohara/github/ohibc/rmd_testing input FALSE a7e123b
table2.csv /Users/caseyohara/github/ohibc/rmd_testing input FALSE a7e123b
table3.csv /Users/caseyohara/github/ohibc/rmd_testing input FALSE a7e123b
tableA.csv /Users/caseyohara/github/ohibc/rmd_testing input FALSE 8b48c04
tableA2.csv /Users/caseyohara input TRUE NA
tableB.csv /Users/caseyohara/github/ohibc/rmd_testing input FALSE 00b6e10
tableC.csv /Users/caseyohara/github/ohibc/rmd_testing input FALSE 00b6e10
table1.csv /Users/caseyohara/github/ohibc/rmd_testing output FALSE 893b676
table1a.csv /Users/caseyohara/github/ohibc/rmd_testing output FALSE a7e123b
table2.csv /Users/caseyohara/github/ohibc/rmd_testing output FALSE a7e123b
table3.csv /Users/caseyohara/github/ohibc/rmd_testing output FALSE a7e123b
tableD.csv /Users/caseyohara/github/ohibc/rmd_testing output FALSE a7e123b
tableE.csv /Users/caseyohara/github/ohibc/rmd_testing output FALSE a7e123b
0_sample_script.Rmd /Users/caseyohara/github/ohibc/rmd_testing/. parent_script TRUE c265b26
1_data_prep_sample.R /Users/caseyohara/github/ohibc/rmd_testing sourced_script FALSE c265b26
1a_gapfill.R /Users/caseyohara/github/ohibc/rmd_testing sourced_script FALSE 725220e
2_model_sample.R /Users/caseyohara/github/ohibc/rmd_testing sourced_script FALSE 725220e